Starting phenix.real_space_refine on Sat Oct 11 23:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.cif Found real_map, /net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.map" model { file = "/net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7koe_22973/10_2025/7koe_22973.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 16 7.16 5 P 12 5.49 5 S 102 5.16 5 C 11690 2.51 5 N 3116 2.21 5 O 3412 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18348 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2195 Classifications: {'peptide': 282} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 264} Chain: "B" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2565 Classifications: {'peptide': 336} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 318} Chain: "C" Number of atoms: 3445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3445 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 17, 'TRANS': 420} Chain: "D" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 746 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'FAD': 1, 'MQ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 8700 SG CYS D 499 45.139 36.362 75.677 1.00 11.68 S ATOM 8723 SG CYS D 502 45.392 41.036 79.247 1.00 10.40 S ATOM 8740 SG CYS D 505 43.304 35.777 80.898 1.00 9.39 S ATOM 8549 SG CYS D 480 40.012 39.136 78.064 1.00 15.00 S ATOM 8457 SG CYS D 467 34.934 28.963 84.782 1.00 26.26 S ATOM 8486 SG CYS D 471 33.932 32.906 88.987 1.00 31.72 S ATOM 8524 SG CYS D 476 36.015 34.470 83.600 1.00 18.30 S ATOM 8772 SG CYS D 509 39.086 32.287 87.448 1.00 17.45 S Restraints were copied for chains: E, F, G, H Time building chain proxies: 5.80, per 1000 atoms: 0.32 Number of scatterers: 18348 At special positions: 0 Unit cell: (99.813, 149.205, 117.306, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 16 26.01 S 102 16.00 P 12 15.00 O 3412 8.00 N 3116 7.00 C 11690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 730.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 D 601 " pdb="FE4 SF4 D 601 " - pdb=" SG CYS D 480 " pdb="FE1 SF4 D 601 " - pdb=" SG CYS D 499 " pdb="FE2 SF4 D 601 " - pdb=" SG CYS D 502 " pdb="FE3 SF4 D 601 " - pdb=" SG CYS D 505 " pdb=" SF4 D 602 " pdb="FE4 SF4 D 602 " - pdb=" SG CYS D 509 " pdb="FE1 SF4 D 602 " - pdb=" SG CYS D 467 " pdb="FE2 SF4 D 602 " - pdb=" SG CYS D 471 " pdb="FE3 SF4 D 602 " - pdb=" SG CYS D 476 " pdb=" SF4 H 601 " pdb="FE4 SF4 H 601 " - pdb=" SG CYS H 480 " pdb="FE1 SF4 H 601 " - pdb=" SG CYS H 499 " pdb="FE2 SF4 H 601 " - pdb=" SG CYS H 502 " pdb="FE3 SF4 H 601 " - pdb=" SG CYS H 505 " pdb=" SF4 H 602 " pdb="FE4 SF4 H 602 " - pdb=" SG CYS H 509 " pdb="FE1 SF4 H 602 " - pdb=" SG CYS H 467 " pdb="FE2 SF4 H 602 " - pdb=" SG CYS H 471 " pdb="FE3 SF4 H 602 " - pdb=" SG CYS H 476 " Number of angles added : 48 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4196 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 32 sheets defined 35.7% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 35 through 53 removed outlier: 3.931A pdb=" N ARG A 40 " --> pdb=" O PRO A 36 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA A 41 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.643A pdb=" N ILE A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 75 " --> pdb=" O LYS A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 109 Processing helix chain 'A' and resid 131 through 140 removed outlier: 3.768A pdb=" N THR A 138 " --> pdb=" O PRO A 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.541A pdb=" N GLY A 216 " --> pdb=" O HIS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 removed outlier: 3.924A pdb=" N GLU A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 258 " --> pdb=" O VAL A 254 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 272 removed outlier: 4.034A pdb=" N VAL A 269 " --> pdb=" O PHE A 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 272 " --> pdb=" O VAL A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 319 removed outlier: 3.610A pdb=" N ASP B 316 " --> pdb=" O GLY B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 346 removed outlier: 4.266A pdb=" N GLU B 341 " --> pdb=" O SER B 337 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 359 removed outlier: 3.596A pdb=" N PHE B 358 " --> pdb=" O ASN B 355 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN B 359 " --> pdb=" O ARG B 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 355 through 359' Processing helix chain 'B' and resid 362 through 370 removed outlier: 3.695A pdb=" N LYS B 368 " --> pdb=" O TYR B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 376 Processing helix chain 'B' and resid 387 through 399 removed outlier: 3.526A pdb=" N MET B 396 " --> pdb=" O GLU B 392 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 491 No H-bonds generated for 'chain 'B' and resid 489 through 491' Processing helix chain 'B' and resid 511 through 523 removed outlier: 3.978A pdb=" N LYS B 515 " --> pdb=" O GLU B 511 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU B 519 " --> pdb=" O LYS B 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 Processing helix chain 'B' and resid 540 through 544 Processing helix chain 'B' and resid 565 through 570 Processing helix chain 'B' and resid 605 through 617 removed outlier: 4.016A pdb=" N LYS B 611 " --> pdb=" O ALA B 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU B 614 " --> pdb=" O ALA B 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 26 removed outlier: 3.517A pdb=" N VAL C 22 " --> pdb=" O SER C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 58 removed outlier: 3.526A pdb=" N ILE C 57 " --> pdb=" O PRO C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 65 Processing helix chain 'C' and resid 108 through 124 removed outlier: 3.629A pdb=" N ARG C 114 " --> pdb=" O ALA C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 175 removed outlier: 3.532A pdb=" N LYS C 174 " --> pdb=" O ILE C 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 175 " --> pdb=" O LEU C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'C' and resid 257 through 266 removed outlier: 3.917A pdb=" N LEU C 261 " --> pdb=" O PRO C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 322 through 344 removed outlier: 3.560A pdb=" N THR C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 361 removed outlier: 3.547A pdb=" N LYS C 359 " --> pdb=" O TYR C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 370 removed outlier: 4.134A pdb=" N LYS C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 370 " --> pdb=" O ASP C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 removed outlier: 3.531A pdb=" N LYS C 379 " --> pdb=" O PRO C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 400 Processing helix chain 'C' and resid 409 through 421 removed outlier: 3.649A pdb=" N ALA C 414 " --> pdb=" O GLN C 410 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 419 " --> pdb=" O ASP C 415 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG C 420 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG C 421 " --> pdb=" O VAL C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 422 through 433 removed outlier: 3.948A pdb=" N LEU C 428 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU C 431 " --> pdb=" O SER C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'D' and resid 440 through 446 removed outlier: 3.943A pdb=" N LYS D 444 " --> pdb=" O ARG D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 496 through 499 Processing helix chain 'D' and resid 503 through 509 removed outlier: 3.526A pdb=" N ILE D 507 " --> pdb=" O GLY D 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 53 removed outlier: 3.931A pdb=" N ARG E 40 " --> pdb=" O PRO E 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 66 through 75 removed outlier: 3.643A pdb=" N ILE E 74 " --> pdb=" O LEU E 70 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA E 75 " --> pdb=" O LYS E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 109 Processing helix chain 'E' and resid 131 through 140 removed outlier: 3.768A pdb=" N THR E 138 " --> pdb=" O PRO E 134 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE E 140 " --> pdb=" O LEU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 204 Processing helix chain 'E' and resid 211 through 216 removed outlier: 3.541A pdb=" N GLY E 216 " --> pdb=" O HIS E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 264 removed outlier: 3.924A pdb=" N GLU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS E 258 " --> pdb=" O VAL E 254 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS E 264 " --> pdb=" O ILE E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 272 removed outlier: 4.034A pdb=" N VAL E 269 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 272 " --> pdb=" O VAL E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 319 removed outlier: 3.610A pdb=" N ASP F 316 " --> pdb=" O GLY F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 346 removed outlier: 4.266A pdb=" N GLU F 341 " --> pdb=" O SER F 337 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE F 343 " --> pdb=" O ALA F 339 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 359 removed outlier: 3.596A pdb=" N PHE F 358 " --> pdb=" O ASN F 355 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN F 359 " --> pdb=" O ARG F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 355 through 359' Processing helix chain 'F' and resid 362 through 370 removed outlier: 3.696A pdb=" N LYS F 368 " --> pdb=" O TYR F 364 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 376 Processing helix chain 'F' and resid 387 through 399 removed outlier: 3.526A pdb=" N MET F 396 " --> pdb=" O GLU F 392 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR F 399 " --> pdb=" O GLY F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 489 through 491 No H-bonds generated for 'chain 'F' and resid 489 through 491' Processing helix chain 'F' and resid 511 through 523 removed outlier: 3.978A pdb=" N LYS F 515 " --> pdb=" O GLU F 511 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU F 519 " --> pdb=" O LYS F 515 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU F 522 " --> pdb=" O GLU F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 535 Processing helix chain 'F' and resid 540 through 544 Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 605 through 617 removed outlier: 4.016A pdb=" N LYS F 611 " --> pdb=" O ALA F 607 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU F 614 " --> pdb=" O ALA F 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 26 removed outlier: 3.517A pdb=" N VAL G 22 " --> pdb=" O SER G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 58 removed outlier: 3.526A pdb=" N ILE G 57 " --> pdb=" O PRO G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.629A pdb=" N ARG G 114 " --> pdb=" O ALA G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 175 removed outlier: 3.532A pdb=" N LYS G 174 " --> pdb=" O ILE G 170 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 175 " --> pdb=" O LEU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 207 Processing helix chain 'G' and resid 222 through 224 No H-bonds generated for 'chain 'G' and resid 222 through 224' Processing helix chain 'G' and resid 247 through 252 Processing helix chain 'G' and resid 257 through 266 removed outlier: 3.917A pdb=" N LEU G 261 " --> pdb=" O PRO G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 309 through 313 Processing helix chain 'G' and resid 322 through 344 removed outlier: 3.560A pdb=" N THR G 328 " --> pdb=" O ASN G 324 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU G 342 " --> pdb=" O LEU G 338 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 361 removed outlier: 3.547A pdb=" N LYS G 359 " --> pdb=" O TYR G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 370 removed outlier: 4.134A pdb=" N LYS G 365 " --> pdb=" O SER G 361 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR G 370 " --> pdb=" O ASP G 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 373 through 379 removed outlier: 3.531A pdb=" N LYS G 379 " --> pdb=" O PRO G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 400 Processing helix chain 'G' and resid 409 through 421 removed outlier: 3.649A pdb=" N ALA G 414 " --> pdb=" O GLN G 410 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER G 419 " --> pdb=" O ASP G 415 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG G 420 " --> pdb=" O MET G 416 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG G 421 " --> pdb=" O VAL G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 422 through 433 removed outlier: 3.948A pdb=" N LEU G 428 " --> pdb=" O ILE G 424 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU G 431 " --> pdb=" O SER G 427 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 438 Processing helix chain 'H' and resid 440 through 446 removed outlier: 3.943A pdb=" N LYS H 444 " --> pdb=" O ARG H 440 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 479 Processing helix chain 'H' and resid 496 through 499 Processing helix chain 'H' and resid 503 through 509 removed outlier: 3.526A pdb=" N ILE H 507 " --> pdb=" O GLY H 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 209 removed outlier: 6.788A pdb=" N VAL A 56 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 82 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 58 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 84 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 60 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 3 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 59 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 5 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N MET A 61 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 2 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 119 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 4 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY A 121 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N CYS A 6 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 118 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 184 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 120 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 143 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 183 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY A 145 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 147 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 164 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL A 162 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 209 removed outlier: 6.788A pdb=" N VAL A 56 " --> pdb=" O GLU A 80 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL A 82 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL A 58 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU A 84 " --> pdb=" O VAL A 58 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A 60 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL A 3 " --> pdb=" O TYR A 57 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 59 " --> pdb=" O VAL A 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 5 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N MET A 61 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN A 2 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU A 119 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL A 4 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY A 121 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N CYS A 6 " --> pdb=" O GLY A 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE A 118 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 184 " --> pdb=" O ILE A 118 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A 120 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA A 143 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR A 183 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY A 145 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR A 147 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL A 164 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE A 151 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL A 162 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 11 Processing sheet with id=AA4, first strand: chain 'A' and resid 17 through 19 removed outlier: 4.141A pdb=" N ARG A 17 " --> pdb=" O VAL A 26 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 230 through 235 removed outlier: 5.166A pdb=" N VAL A 231 " --> pdb=" O MET B 437 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET B 437 " --> pdb=" O VAL A 231 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 326 removed outlier: 8.280A pdb=" N LEU B 383 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE B 293 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY B 385 " --> pdb=" O PHE B 293 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE B 382 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL B 448 " --> pdb=" O PHE B 382 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE B 384 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET B 445 " --> pdb=" O LEU B 405 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA B 407 " --> pdb=" O MET B 445 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR B 447 " --> pdb=" O ALA B 407 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 298 through 299 removed outlier: 3.734A pdb=" N LYS B 302 " --> pdb=" O HIS B 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.635A pdb=" N VAL B 350 " --> pdb=" O ILE B 467 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU B 469 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR B 352 " --> pdb=" O GLU B 469 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 526 through 529 removed outlier: 6.116A pdb=" N VAL B 499 " --> pdb=" O GLU B 526 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY B 528 " --> pdb=" O VAL B 499 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 501 " --> pdb=" O GLY B 528 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR B 557 " --> pdb=" O VAL B 579 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE B 581 " --> pdb=" O TYR B 557 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA B 559 " --> pdb=" O ILE B 581 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE B 578 " --> pdb=" O ILE B 595 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE B 597 " --> pdb=" O ILE B 578 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA B 580 " --> pdb=" O ILE B 597 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 4 removed outlier: 6.460A pdb=" N ILE C 3 " --> pdb=" O HIS C 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 135 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 126 through 128 removed outlier: 6.788A pdb=" N VAL C 30 " --> pdb=" O LEU C 126 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE C 128 " --> pdb=" O VAL C 30 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL C 32 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL C 8 " --> pdb=" O VAL C 162 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 50 removed outlier: 4.657A pdb=" N ALA C 104 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 106 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 73 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY C 213 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN C 74 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR C 215 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE C 76 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 12.629A pdb=" N GLU C 217 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLN C 78 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N LEU C 219 " --> pdb=" O GLN C 78 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ALA C 214 " --> pdb=" O ALA C 234 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 49 through 50 removed outlier: 4.657A pdb=" N ALA C 104 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR C 106 " --> pdb=" O ARG C 73 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG C 73 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLY C 213 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN C 74 " --> pdb=" O GLY C 213 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR C 215 " --> pdb=" O ASN C 74 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE C 76 " --> pdb=" O THR C 215 " (cutoff:3.500A) removed outlier: 12.629A pdb=" N GLU C 217 " --> pdb=" O ILE C 76 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLN C 78 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N LEU C 219 " --> pdb=" O GLN C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 94 through 95 removed outlier: 6.294A pdb=" N GLY G 213 " --> pdb=" O GLU G 72 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ASN G 74 " --> pdb=" O GLY G 213 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N THR G 215 " --> pdb=" O ASN G 74 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ILE G 76 " --> pdb=" O THR G 215 " (cutoff:3.500A) removed outlier: 12.629A pdb=" N GLU G 217 " --> pdb=" O ILE G 76 " (cutoff:3.500A) removed outlier: 10.186A pdb=" N GLN G 78 " --> pdb=" O GLU G 217 " (cutoff:3.500A) removed outlier: 12.040A pdb=" N LEU G 219 " --> pdb=" O GLN G 78 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG G 73 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR G 106 " --> pdb=" O ARG G 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA G 104 " --> pdb=" O VAL G 75 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.213A pdb=" N ALA G 214 " --> pdb=" O ALA G 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 450 through 451 Processing sheet with id=AB8, first strand: chain 'D' and resid 459 through 460 Processing sheet with id=AB9, first strand: chain 'D' and resid 485 through 488 removed outlier: 3.599A pdb=" N GLY D 491 " --> pdb=" O THR D 488 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 208 through 209 removed outlier: 6.788A pdb=" N VAL E 56 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL E 82 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU E 84 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 60 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 3 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 59 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 5 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N MET E 61 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN E 2 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU E 119 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 4 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY E 121 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N CYS E 6 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 118 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE E 184 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 120 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA E 143 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR E 183 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY E 145 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR E 147 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 164 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 151 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL E 162 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 208 through 209 removed outlier: 6.788A pdb=" N VAL E 56 " --> pdb=" O GLU E 80 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N VAL E 82 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL E 58 " --> pdb=" O VAL E 82 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N LEU E 84 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR E 60 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL E 3 " --> pdb=" O TYR E 57 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 59 " --> pdb=" O VAL E 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL E 5 " --> pdb=" O ILE E 59 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N MET E 61 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ASN E 2 " --> pdb=" O LEU E 117 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU E 119 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL E 4 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N GLY E 121 " --> pdb=" O VAL E 4 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N CYS E 6 " --> pdb=" O GLY E 121 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ILE E 118 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE E 184 " --> pdb=" O ILE E 118 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 120 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA E 143 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N THR E 183 " --> pdb=" O ALA E 143 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N GLY E 145 " --> pdb=" O THR E 183 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N TYR E 147 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL E 164 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ILE E 151 " --> pdb=" O VAL E 162 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL E 162 " --> pdb=" O ILE E 151 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 9 through 11 Processing sheet with id=AC4, first strand: chain 'E' and resid 17 through 19 removed outlier: 4.141A pdb=" N ARG E 17 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 230 through 235 removed outlier: 5.166A pdb=" N VAL E 231 " --> pdb=" O MET F 437 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N MET F 437 " --> pdb=" O VAL E 231 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 325 through 326 removed outlier: 8.280A pdb=" N LEU F 383 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N PHE F 293 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY F 385 " --> pdb=" O PHE F 293 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE F 382 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N VAL F 448 " --> pdb=" O PHE F 382 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE F 384 " --> pdb=" O VAL F 448 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N MET F 445 " --> pdb=" O LEU F 405 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ALA F 407 " --> pdb=" O MET F 445 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N THR F 447 " --> pdb=" O ALA F 407 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 298 through 299 removed outlier: 3.734A pdb=" N LYS F 302 " --> pdb=" O HIS F 299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 329 through 331 removed outlier: 6.635A pdb=" N VAL F 350 " --> pdb=" O ILE F 467 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLU F 469 " --> pdb=" O VAL F 350 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR F 352 " --> pdb=" O GLU F 469 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 526 through 529 removed outlier: 6.116A pdb=" N VAL F 499 " --> pdb=" O GLU F 526 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLY F 528 " --> pdb=" O VAL F 499 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 501 " --> pdb=" O GLY F 528 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N TYR F 557 " --> pdb=" O VAL F 579 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE F 581 " --> pdb=" O TYR F 557 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ALA F 559 " --> pdb=" O ILE F 581 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ILE F 578 " --> pdb=" O ILE F 595 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE F 597 " --> pdb=" O ILE F 578 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ALA F 580 " --> pdb=" O ILE F 597 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 4 removed outlier: 6.460A pdb=" N ILE G 3 " --> pdb=" O HIS G 157 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP G 135 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 126 through 128 removed outlier: 6.788A pdb=" N VAL G 30 " --> pdb=" O LEU G 126 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ILE G 128 " --> pdb=" O VAL G 30 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N VAL G 32 " --> pdb=" O ILE G 128 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL G 8 " --> pdb=" O VAL G 162 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL G 305 " --> pdb=" O GLY G 302 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 450 through 451 Processing sheet with id=AD4, first strand: chain 'H' and resid 459 through 460 Processing sheet with id=AD5, first strand: chain 'H' and resid 485 through 488 removed outlier: 3.599A pdb=" N GLY H 491 " --> pdb=" O THR H 488 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.62 Time building geometry restraints manager: 1.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.40: 7296 1.40 - 1.58: 11236 1.58 - 1.77: 14 1.77 - 1.95: 136 1.95 - 2.14: 48 Bond restraints: 18730 Sorted by residual: bond pdb=" C17 MQ7 G 502 " pdb=" C18 MQ7 G 502 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C17 MQ7 C 502 " pdb=" C18 MQ7 C 502 " ideal model delta sigma weight residual 1.336 1.557 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C12 MQ7 C 502 " pdb=" C13 MQ7 C 502 " ideal model delta sigma weight residual 1.335 1.552 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C12 MQ7 G 502 " pdb=" C13 MQ7 G 502 " ideal model delta sigma weight residual 1.335 1.552 -0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C32 MQ7 G 502 " pdb=" C33 MQ7 G 502 " ideal model delta sigma weight residual 1.336 1.553 -0.217 2.00e-02 2.50e+03 1.18e+02 ... (remaining 18725 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 24904 3.27 - 6.54: 328 6.54 - 9.81: 48 9.81 - 13.07: 16 13.07 - 16.34: 110 Bond angle restraints: 25406 Sorted by residual: angle pdb="FE2 SF4 D 601 " pdb=" S1 SF4 D 601 " pdb="FE4 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE2 SF4 H 601 " pdb=" S1 SF4 H 601 " pdb="FE4 SF4 H 601 " ideal model delta sigma weight residual 73.70 90.03 -16.33 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 D 601 " pdb=" S4 SF4 D 601 " pdb="FE3 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE1 SF4 H 601 " pdb=" S4 SF4 H 601 " pdb="FE3 SF4 H 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 angle pdb="FE2 SF4 D 601 " pdb=" S3 SF4 D 601 " pdb="FE4 SF4 D 601 " ideal model delta sigma weight residual 73.70 90.02 -16.32 1.50e+00 4.44e-01 1.18e+02 ... (remaining 25401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 11034 35.02 - 70.03: 370 70.03 - 105.04: 22 105.04 - 140.06: 0 140.06 - 175.07: 4 Dihedral angle restraints: 11430 sinusoidal: 4876 harmonic: 6554 Sorted by residual: dihedral pdb=" CA VAL C 197 " pdb=" C VAL C 197 " pdb=" N PRO C 198 " pdb=" CA PRO C 198 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA VAL G 197 " pdb=" C VAL G 197 " pdb=" N PRO G 198 " pdb=" CA PRO G 198 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA PRO C 198 " pdb=" C PRO C 198 " pdb=" N GLU C 199 " pdb=" CA GLU C 199 " ideal model delta harmonic sigma weight residual 180.00 154.29 25.71 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 11427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.166: 2798 0.166 - 0.331: 28 0.331 - 0.497: 2 0.497 - 0.662: 0 0.662 - 0.828: 16 Chirality restraints: 2844 Sorted by residual: chirality pdb="FE1 SF4 D 602 " pdb=" S2 SF4 D 602 " pdb=" S3 SF4 D 602 " pdb=" S4 SF4 D 602 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE1 SF4 H 602 " pdb=" S2 SF4 H 602 " pdb=" S3 SF4 H 602 " pdb=" S4 SF4 H 602 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.83 2.00e-01 2.50e+01 1.71e+01 chirality pdb="FE3 SF4 D 601 " pdb=" S1 SF4 D 601 " pdb=" S2 SF4 D 601 " pdb=" S4 SF4 D 601 " both_signs ideal model delta sigma weight residual False -10.55 -9.73 -0.82 2.00e-01 2.50e+01 1.70e+01 ... (remaining 2841 not shown) Planarity restraints: 3200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 MQ7 G 502 " 0.248 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C12 MQ7 G 502 " -0.516 2.00e-02 2.50e+03 pdb=" C13 MQ7 G 502 " 0.293 2.00e-02 2.50e+03 pdb=" C14 MQ7 G 502 " 0.021 2.00e-02 2.50e+03 pdb=" C15 MQ7 G 502 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 MQ7 C 502 " -0.248 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C12 MQ7 C 502 " 0.516 2.00e-02 2.50e+03 pdb=" C13 MQ7 C 502 " -0.293 2.00e-02 2.50e+03 pdb=" C14 MQ7 C 502 " -0.021 2.00e-02 2.50e+03 pdb=" C15 MQ7 C 502 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C31 MQ7 G 502 " -0.149 2.00e-02 2.50e+03 2.27e-01 6.43e+02 pdb=" C32 MQ7 G 502 " 0.329 2.00e-02 2.50e+03 pdb=" C33 MQ7 G 502 " -0.327 2.00e-02 2.50e+03 pdb=" C34 MQ7 G 502 " 0.141 2.00e-02 2.50e+03 pdb=" C35 MQ7 G 502 " 0.005 2.00e-02 2.50e+03 ... (remaining 3197 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 198 2.57 - 3.15: 13520 3.15 - 3.73: 29598 3.73 - 4.32: 45024 4.32 - 4.90: 73202 Nonbonded interactions: 161542 Sorted by model distance: nonbonded pdb=" O CYS E 6 " pdb=" O2B FAD E 301 " model vdw 1.984 3.040 nonbonded pdb=" O CYS A 6 " pdb=" O2B FAD A 301 " model vdw 1.984 3.040 nonbonded pdb=" OG1 THR A 97 " pdb=" O4' FAD A 301 " model vdw 2.002 3.040 nonbonded pdb=" OG1 THR E 97 " pdb=" O4' FAD E 301 " model vdw 2.002 3.040 nonbonded pdb=" O GLY E 127 " pdb=" O1P FAD E 301 " model vdw 2.045 3.040 ... (remaining 161537 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.740 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.641 18746 Z= 0.710 Angle : 1.638 38.599 25454 Z= 0.834 Chirality : 0.085 0.828 2844 Planarity : 0.016 0.288 3200 Dihedral : 16.975 175.074 7234 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.71 % Favored : 93.20 % Rotamer: Outliers : 2.18 % Allowed : 7.48 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.90 (0.13), residues: 2280 helix: -4.48 (0.08), residues: 776 sheet: -2.25 (0.22), residues: 404 loop : -2.60 (0.15), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 320 TYR 0.021 0.002 TYR B 352 PHE 0.018 0.002 PHE B 476 TRP 0.013 0.002 TRP B 327 HIS 0.004 0.001 HIS C 267 Details of bonding type rmsd covalent geometry : bond 0.01297 (18730) covalent geometry : angle 1.42189 (25406) hydrogen bonds : bond 0.26331 ( 574) hydrogen bonds : angle 10.13710 ( 1689) metal coordination : bond 0.49359 ( 16) metal coordination : angle 18.76354 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 0.657 Fit side-chains REVERT: A 142 TYR cc_start: 0.8560 (m-10) cc_final: 0.8355 (m-10) REVERT: A 152 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: A 245 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7421 (mm) REVERT: C 291 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6732 (mt-10) REVERT: C 370 TYR cc_start: 0.8636 (m-80) cc_final: 0.8406 (m-80) REVERT: C 371 LYS cc_start: 0.8240 (ttpt) cc_final: 0.8007 (ttpp) REVERT: C 390 LEU cc_start: 0.8571 (tt) cc_final: 0.8350 (tp) REVERT: C 435 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7049 (ptm160) REVERT: D 465 SER cc_start: 0.8103 (p) cc_final: 0.7578 (p) REVERT: D 517 ASN cc_start: 0.8194 (m-40) cc_final: 0.7979 (m110) REVERT: E 142 TYR cc_start: 0.8560 (m-10) cc_final: 0.8353 (m-10) REVERT: E 152 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7080 (mm-30) REVERT: E 245 ILE cc_start: 0.7730 (OUTLIER) cc_final: 0.7418 (mm) REVERT: G 291 GLU cc_start: 0.6949 (mt-10) cc_final: 0.6730 (mt-10) REVERT: G 370 TYR cc_start: 0.8634 (m-80) cc_final: 0.8404 (m-80) REVERT: G 371 LYS cc_start: 0.8237 (ttpt) cc_final: 0.8005 (ttpp) REVERT: G 390 LEU cc_start: 0.8571 (tt) cc_final: 0.8351 (tp) REVERT: G 435 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7046 (ptm160) REVERT: H 465 SER cc_start: 0.8101 (p) cc_final: 0.7581 (p) REVERT: H 517 ASN cc_start: 0.8187 (m-40) cc_final: 0.7977 (m110) outliers start: 42 outliers final: 14 residues processed: 392 average time/residue: 0.7626 time to fit residues: 328.9540 Evaluate side-chains 256 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 159 LYS Chi-restraints excluded: chain A residue 245 ILE Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 251 ASP Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 471 CYS Chi-restraints excluded: chain E residue 152 GLU Chi-restraints excluded: chain E residue 153 GLU Chi-restraints excluded: chain E residue 159 LYS Chi-restraints excluded: chain E residue 245 ILE Chi-restraints excluded: chain E residue 248 LYS Chi-restraints excluded: chain E residue 251 ASP Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 471 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 212 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN B 359 ASN C 79 ASN C 101 ASN C 118 GLN C 168 ASN C 203 ASN C 324 ASN C 392 ASN C 412 GLN D 448 ASN E 15 ASN F 359 ASN G 79 ASN G 101 ASN G 118 GLN G 168 ASN G 203 ASN G 324 ASN G 392 ASN G 412 GLN H 448 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.160267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.120938 restraints weight = 20387.664| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.79 r_work: 0.3136 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18746 Z= 0.177 Angle : 0.704 16.602 25454 Z= 0.324 Chirality : 0.047 0.176 2844 Planarity : 0.006 0.068 3200 Dihedral : 13.533 155.406 2846 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.88 % Favored : 94.04 % Rotamer: Outliers : 2.70 % Allowed : 16.48 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.76 (0.15), residues: 2280 helix: -2.94 (0.14), residues: 794 sheet: -2.22 (0.22), residues: 438 loop : -2.10 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 451 TYR 0.015 0.002 TYR G 370 PHE 0.014 0.002 PHE G 112 TRP 0.010 0.001 TRP A 103 HIS 0.004 0.001 HIS B 298 Details of bonding type rmsd covalent geometry : bond 0.00407 (18730) covalent geometry : angle 0.62807 (25406) hydrogen bonds : bond 0.04105 ( 574) hydrogen bonds : angle 6.12388 ( 1689) metal coordination : bond 0.01626 ( 16) metal coordination : angle 7.34751 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 255 time to evaluate : 0.727 Fit side-chains REVERT: A 43 GLU cc_start: 0.8491 (tp30) cc_final: 0.8258 (tp30) REVERT: A 142 TYR cc_start: 0.8772 (m-10) cc_final: 0.8519 (m-10) REVERT: A 154 ILE cc_start: 0.7351 (OUTLIER) cc_final: 0.6977 (mt) REVERT: B 396 MET cc_start: 0.7718 (mtp) cc_final: 0.7382 (mtp) REVERT: C 266 ASN cc_start: 0.8709 (m-40) cc_final: 0.8416 (m-40) REVERT: C 274 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7409 (mt) REVERT: C 291 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7161 (mt-10) REVERT: C 295 TYR cc_start: 0.8712 (m-10) cc_final: 0.8467 (m-10) REVERT: C 320 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7830 (tmm160) REVERT: C 339 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7495 (pt0) REVERT: C 371 LYS cc_start: 0.8099 (ttpt) cc_final: 0.7479 (ttpp) REVERT: C 372 ASP cc_start: 0.7963 (m-30) cc_final: 0.7645 (m-30) REVERT: D 451 ARG cc_start: 0.9009 (ttm-80) cc_final: 0.8730 (ttm-80) REVERT: D 460 LYS cc_start: 0.8425 (ttpp) cc_final: 0.7799 (mppt) REVERT: D 470 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8386 (mtpt) REVERT: E 43 GLU cc_start: 0.8489 (tp30) cc_final: 0.8242 (tp30) REVERT: E 142 TYR cc_start: 0.8767 (m-10) cc_final: 0.8515 (m-10) REVERT: E 154 ILE cc_start: 0.7336 (OUTLIER) cc_final: 0.6962 (mt) REVERT: F 396 MET cc_start: 0.7718 (mtp) cc_final: 0.7387 (mtp) REVERT: G 177 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7138 (mt) REVERT: G 266 ASN cc_start: 0.8717 (m-40) cc_final: 0.8426 (m-40) REVERT: G 274 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7394 (mt) REVERT: G 291 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7156 (mt-10) REVERT: G 295 TYR cc_start: 0.8717 (m-10) cc_final: 0.8475 (m-10) REVERT: G 320 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (tmm160) REVERT: G 339 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7505 (pt0) REVERT: G 371 LYS cc_start: 0.8095 (ttpt) cc_final: 0.7469 (ttpp) REVERT: G 372 ASP cc_start: 0.7968 (m-30) cc_final: 0.7661 (m-30) REVERT: H 451 ARG cc_start: 0.9008 (ttm-80) cc_final: 0.8730 (ttm-80) REVERT: H 460 LYS cc_start: 0.8427 (ttpp) cc_final: 0.7801 (mppt) REVERT: H 470 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8386 (mtpt) outliers start: 52 outliers final: 20 residues processed: 291 average time/residue: 0.6559 time to fit residues: 213.1366 Evaluate side-chains 251 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 224 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 320 ARG Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 320 ARG Chi-restraints excluded: chain G residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 82 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 225 optimal weight: 0.0570 chunk 43 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 324 ASN E 23 ASN F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118853 restraints weight = 20717.007| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.69 r_work: 0.3158 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18746 Z= 0.166 Angle : 0.664 14.521 25454 Z= 0.303 Chirality : 0.047 0.179 2844 Planarity : 0.005 0.056 3200 Dihedral : 12.857 149.464 2800 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.22 % Allowed : 18.45 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.01 (0.15), residues: 2280 helix: -1.92 (0.16), residues: 780 sheet: -2.07 (0.22), residues: 438 loop : -1.89 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 451 TYR 0.012 0.001 TYR C 50 PHE 0.012 0.001 PHE C 112 TRP 0.012 0.001 TRP E 103 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00386 (18730) covalent geometry : angle 0.59409 (25406) hydrogen bonds : bond 0.03727 ( 574) hydrogen bonds : angle 5.67929 ( 1689) metal coordination : bond 0.01588 ( 16) metal coordination : angle 6.87069 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 238 time to evaluate : 0.699 Fit side-chains REVERT: A 43 GLU cc_start: 0.8469 (tp30) cc_final: 0.8267 (tp30) REVERT: A 142 TYR cc_start: 0.8774 (m-10) cc_final: 0.8527 (m-10) REVERT: A 154 ILE cc_start: 0.7282 (OUTLIER) cc_final: 0.6933 (mt) REVERT: B 374 VAL cc_start: 0.8608 (t) cc_final: 0.8311 (m) REVERT: B 396 MET cc_start: 0.7846 (mtp) cc_final: 0.7544 (mtp) REVERT: C 97 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8274 (tm-30) REVERT: C 266 ASN cc_start: 0.8709 (m-40) cc_final: 0.8445 (m-40) REVERT: C 274 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7415 (mt) REVERT: C 339 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7570 (pt0) REVERT: C 371 LYS cc_start: 0.8082 (ttpt) cc_final: 0.7438 (ttpp) REVERT: C 372 ASP cc_start: 0.7949 (m-30) cc_final: 0.7378 (m-30) REVERT: D 460 LYS cc_start: 0.8409 (ttpp) cc_final: 0.7844 (mppt) REVERT: D 470 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8445 (mtpt) REVERT: E 43 GLU cc_start: 0.8469 (tp30) cc_final: 0.8265 (tp30) REVERT: E 142 TYR cc_start: 0.8776 (m-10) cc_final: 0.8523 (m-10) REVERT: E 154 ILE cc_start: 0.7283 (OUTLIER) cc_final: 0.6915 (mt) REVERT: F 374 VAL cc_start: 0.8603 (t) cc_final: 0.8301 (m) REVERT: F 396 MET cc_start: 0.7846 (mtp) cc_final: 0.7546 (mtp) REVERT: G 97 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8265 (tm-30) REVERT: G 229 MET cc_start: 0.8881 (ttp) cc_final: 0.8652 (ttp) REVERT: G 266 ASN cc_start: 0.8722 (m-40) cc_final: 0.8461 (m-40) REVERT: G 274 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7403 (mt) REVERT: G 339 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7567 (pt0) REVERT: G 371 LYS cc_start: 0.8074 (ttpt) cc_final: 0.7420 (ttpp) REVERT: G 372 ASP cc_start: 0.7952 (m-30) cc_final: 0.7387 (m-30) REVERT: H 460 LYS cc_start: 0.8419 (ttpp) cc_final: 0.7849 (mppt) REVERT: H 470 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8450 (mtpt) outliers start: 62 outliers final: 26 residues processed: 286 average time/residue: 0.6160 time to fit residues: 197.9153 Evaluate side-chains 261 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 98 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 211 optimal weight: 0.8980 chunk 156 optimal weight: 0.5980 chunk 175 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 324 ASN F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.121159 restraints weight = 20380.017| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.84 r_work: 0.3140 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18746 Z= 0.168 Angle : 0.654 13.301 25454 Z= 0.300 Chirality : 0.047 0.182 2844 Planarity : 0.005 0.055 3200 Dihedral : 12.540 146.359 2800 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.74 % Allowed : 19.75 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.59 (0.16), residues: 2280 helix: -1.29 (0.17), residues: 790 sheet: -1.93 (0.22), residues: 440 loop : -1.85 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 87 TYR 0.011 0.002 TYR C 370 PHE 0.013 0.001 PHE F 382 TRP 0.011 0.001 TRP E 103 HIS 0.003 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00394 (18730) covalent geometry : angle 0.59028 (25406) hydrogen bonds : bond 0.03431 ( 574) hydrogen bonds : angle 5.44747 ( 1689) metal coordination : bond 0.01411 ( 16) metal coordination : angle 6.51446 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 234 time to evaluate : 0.672 Fit side-chains REVERT: A 142 TYR cc_start: 0.8799 (m-10) cc_final: 0.8563 (m-10) REVERT: A 154 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6914 (mt) REVERT: B 374 VAL cc_start: 0.8588 (t) cc_final: 0.8253 (m) REVERT: B 396 MET cc_start: 0.7931 (mtp) cc_final: 0.7669 (mtp) REVERT: C 266 ASN cc_start: 0.8685 (m-40) cc_final: 0.8467 (m-40) REVERT: C 274 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7482 (mt) REVERT: C 339 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7578 (pt0) REVERT: C 371 LYS cc_start: 0.8143 (ttpt) cc_final: 0.7562 (ttpp) REVERT: C 393 ASP cc_start: 0.8288 (m-30) cc_final: 0.7931 (m-30) REVERT: C 431 LEU cc_start: 0.5792 (OUTLIER) cc_final: 0.4991 (pt) REVERT: C 435 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.6585 (mtm180) REVERT: D 460 LYS cc_start: 0.8504 (ttpp) cc_final: 0.7885 (mppt) REVERT: D 470 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8430 (mtpt) REVERT: E 142 TYR cc_start: 0.8805 (m-10) cc_final: 0.8567 (m-10) REVERT: E 154 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.6909 (mt) REVERT: F 374 VAL cc_start: 0.8581 (t) cc_final: 0.8239 (m) REVERT: F 396 MET cc_start: 0.7926 (mtp) cc_final: 0.7667 (mtp) REVERT: G 274 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7477 (mt) REVERT: G 295 TYR cc_start: 0.8520 (m-10) cc_final: 0.8320 (m-10) REVERT: G 371 LYS cc_start: 0.8126 (ttpt) cc_final: 0.7512 (ttpp) REVERT: G 393 ASP cc_start: 0.8284 (m-30) cc_final: 0.7924 (m-30) REVERT: G 431 LEU cc_start: 0.5791 (OUTLIER) cc_final: 0.4990 (pt) REVERT: G 435 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6591 (mtm180) REVERT: H 460 LYS cc_start: 0.8511 (ttpp) cc_final: 0.7895 (mppt) REVERT: H 470 LYS cc_start: 0.8668 (mtmt) cc_final: 0.8409 (mtpt) outliers start: 72 outliers final: 32 residues processed: 286 average time/residue: 0.5907 time to fit residues: 190.1813 Evaluate side-chains 266 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 226 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 478 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 162 optimal weight: 0.0770 chunk 210 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 324 ASN F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.156586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.113836 restraints weight = 20444.239| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.92 r_work: 0.3169 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18746 Z= 0.205 Angle : 0.670 13.099 25454 Z= 0.310 Chirality : 0.048 0.186 2844 Planarity : 0.005 0.059 3200 Dihedral : 12.577 145.101 2800 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.00 % Allowed : 19.75 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.16), residues: 2280 helix: -0.99 (0.18), residues: 792 sheet: -1.94 (0.22), residues: 442 loop : -1.70 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 451 TYR 0.012 0.002 TYR C 50 PHE 0.014 0.002 PHE B 382 TRP 0.010 0.001 TRP E 103 HIS 0.004 0.001 HIS C 93 Details of bonding type rmsd covalent geometry : bond 0.00481 (18730) covalent geometry : angle 0.61312 (25406) hydrogen bonds : bond 0.03497 ( 574) hydrogen bonds : angle 5.43323 ( 1689) metal coordination : bond 0.01818 ( 16) metal coordination : angle 6.25684 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8839 (m-10) cc_final: 0.8619 (m-10) REVERT: A 154 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6912 (mt) REVERT: A 186 ASP cc_start: 0.7895 (m-30) cc_final: 0.7608 (m-30) REVERT: B 374 VAL cc_start: 0.8653 (t) cc_final: 0.8275 (m) REVERT: C 86 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8072 (pm20) REVERT: C 97 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8465 (pp20) REVERT: C 165 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8413 (pp20) REVERT: C 180 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8110 (tt0) REVERT: C 229 MET cc_start: 0.8735 (ttm) cc_final: 0.8477 (ttp) REVERT: C 274 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7633 (mt) REVERT: C 371 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7660 (ttpp) REVERT: C 393 ASP cc_start: 0.8335 (m-30) cc_final: 0.7961 (m-30) REVERT: C 431 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5072 (pt) REVERT: C 435 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.6639 (mtm180) REVERT: D 460 LYS cc_start: 0.8535 (ttpp) cc_final: 0.7971 (mppt) REVERT: D 469 GLU cc_start: 0.8576 (pm20) cc_final: 0.8360 (pm20) REVERT: D 470 LYS cc_start: 0.8707 (mtmt) cc_final: 0.8464 (mtpt) REVERT: E 142 TYR cc_start: 0.8841 (m-10) cc_final: 0.8630 (m-10) REVERT: E 154 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6890 (mt) REVERT: E 186 ASP cc_start: 0.7885 (m-30) cc_final: 0.7596 (m-30) REVERT: F 374 VAL cc_start: 0.8639 (t) cc_final: 0.8268 (m) REVERT: G 86 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.8071 (pm20) REVERT: G 97 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8435 (pp20) REVERT: G 165 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8396 (pp20) REVERT: G 180 GLU cc_start: 0.8365 (mt-10) cc_final: 0.8069 (tt0) REVERT: G 229 MET cc_start: 0.8727 (ttm) cc_final: 0.8468 (ttp) REVERT: G 274 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7644 (mt) REVERT: G 371 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7536 (ttpp) REVERT: G 431 LEU cc_start: 0.5902 (OUTLIER) cc_final: 0.5064 (pt) REVERT: G 435 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6637 (mtm180) REVERT: H 460 LYS cc_start: 0.8537 (ttpp) cc_final: 0.7988 (mppt) REVERT: H 469 GLU cc_start: 0.8574 (pm20) cc_final: 0.8357 (pm20) REVERT: H 470 LYS cc_start: 0.8704 (mtmt) cc_final: 0.8460 (mtpt) outliers start: 77 outliers final: 36 residues processed: 293 average time/residue: 0.6564 time to fit residues: 215.7381 Evaluate side-chains 265 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 86 GLU Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 165 GLU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 45 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 161 optimal weight: 0.0470 chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 187 optimal weight: 0.9980 chunk 205 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 185 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.157224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.118145 restraints weight = 20500.283| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.68 r_work: 0.3150 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 18746 Z= 0.157 Angle : 0.639 12.524 25454 Z= 0.293 Chirality : 0.047 0.185 2844 Planarity : 0.004 0.055 3200 Dihedral : 12.402 146.056 2800 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.85 % Allowed : 20.74 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.17), residues: 2280 helix: -0.76 (0.18), residues: 790 sheet: -1.94 (0.22), residues: 446 loop : -1.61 (0.18), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 451 TYR 0.012 0.001 TYR C 295 PHE 0.011 0.001 PHE C 112 TRP 0.009 0.001 TRP E 103 HIS 0.004 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00366 (18730) covalent geometry : angle 0.58000 (25406) hydrogen bonds : bond 0.03256 ( 574) hydrogen bonds : angle 5.30531 ( 1689) metal coordination : bond 0.01127 ( 16) metal coordination : angle 6.22958 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 231 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8776 (m-10) cc_final: 0.8542 (m-10) REVERT: A 154 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6921 (mt) REVERT: A 186 ASP cc_start: 0.7938 (m-30) cc_final: 0.7636 (m-30) REVERT: B 373 MET cc_start: 0.7292 (mmt) cc_final: 0.7078 (mpm) REVERT: C 229 MET cc_start: 0.8599 (ttm) cc_final: 0.8305 (ttp) REVERT: C 274 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7457 (mt) REVERT: C 371 LYS cc_start: 0.8153 (ttpt) cc_final: 0.7631 (ttpp) REVERT: C 393 ASP cc_start: 0.8176 (m-30) cc_final: 0.7794 (m-30) REVERT: C 431 LEU cc_start: 0.5715 (OUTLIER) cc_final: 0.5030 (pt) REVERT: C 435 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6632 (mtm180) REVERT: D 460 LYS cc_start: 0.8405 (ttpp) cc_final: 0.7796 (mppt) REVERT: D 469 GLU cc_start: 0.8505 (pm20) cc_final: 0.8292 (pm20) REVERT: D 470 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8434 (mtpt) REVERT: E 142 TYR cc_start: 0.8774 (m-10) cc_final: 0.8539 (m-10) REVERT: E 154 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6915 (mt) REVERT: E 186 ASP cc_start: 0.7940 (m-30) cc_final: 0.7633 (m-30) REVERT: F 373 MET cc_start: 0.7270 (mmt) cc_final: 0.7055 (mpm) REVERT: G 229 MET cc_start: 0.8588 (ttm) cc_final: 0.8319 (ttp) REVERT: G 274 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7457 (mt) REVERT: G 371 LYS cc_start: 0.8118 (ttpt) cc_final: 0.7594 (ttpp) REVERT: G 393 ASP cc_start: 0.8182 (m-30) cc_final: 0.7791 (m-30) REVERT: G 431 LEU cc_start: 0.5714 (OUTLIER) cc_final: 0.5030 (pt) REVERT: G 435 ARG cc_start: 0.7667 (OUTLIER) cc_final: 0.6635 (mtm180) REVERT: H 451 ARG cc_start: 0.8962 (ttm-80) cc_final: 0.8737 (ttm170) REVERT: H 460 LYS cc_start: 0.8412 (ttpp) cc_final: 0.7803 (mppt) REVERT: H 470 LYS cc_start: 0.8679 (mtmt) cc_final: 0.8437 (mtpt) outliers start: 74 outliers final: 37 residues processed: 288 average time/residue: 0.6348 time to fit residues: 205.0368 Evaluate side-chains 264 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 198 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 29 optimal weight: 0.0060 chunk 91 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 218 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 324 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 324 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.161050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.120194 restraints weight = 20358.587| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.83 r_work: 0.3072 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18746 Z= 0.188 Angle : 0.658 12.284 25454 Z= 0.305 Chirality : 0.048 0.185 2844 Planarity : 0.004 0.060 3200 Dihedral : 12.428 146.137 2800 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.16 % Allowed : 20.95 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.10 (0.17), residues: 2280 helix: -0.68 (0.18), residues: 792 sheet: -1.94 (0.22), residues: 448 loop : -1.59 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 451 TYR 0.015 0.002 TYR G 295 PHE 0.012 0.002 PHE C 112 TRP 0.009 0.001 TRP A 103 HIS 0.004 0.001 HIS C 319 Details of bonding type rmsd covalent geometry : bond 0.00443 (18730) covalent geometry : angle 0.60560 (25406) hydrogen bonds : bond 0.03378 ( 574) hydrogen bonds : angle 5.34387 ( 1689) metal coordination : bond 0.01548 ( 16) metal coordination : angle 5.98058 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 221 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8790 (m-10) cc_final: 0.8562 (m-10) REVERT: A 154 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6906 (mt) REVERT: A 186 ASP cc_start: 0.7866 (m-30) cc_final: 0.7565 (m-30) REVERT: A 273 GLU cc_start: 0.7012 (OUTLIER) cc_final: 0.6481 (tp30) REVERT: B 373 MET cc_start: 0.7343 (mmt) cc_final: 0.6910 (mpm) REVERT: C 180 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8037 (tt0) REVERT: C 229 MET cc_start: 0.8743 (ttm) cc_final: 0.8467 (ttp) REVERT: C 274 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7521 (mt) REVERT: C 371 LYS cc_start: 0.8149 (ttpt) cc_final: 0.7757 (ttpp) REVERT: C 393 ASP cc_start: 0.8220 (m-30) cc_final: 0.7831 (m-30) REVERT: C 431 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5035 (pt) REVERT: C 435 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6635 (mtm180) REVERT: D 460 LYS cc_start: 0.8515 (ttpp) cc_final: 0.7833 (mppt) REVERT: D 470 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8377 (mtpt) REVERT: E 142 TYR cc_start: 0.8790 (m-10) cc_final: 0.8563 (m-10) REVERT: E 154 ILE cc_start: 0.7268 (OUTLIER) cc_final: 0.6893 (mt) REVERT: E 186 ASP cc_start: 0.7878 (m-30) cc_final: 0.7574 (m-30) REVERT: E 273 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6486 (tp30) REVERT: F 373 MET cc_start: 0.7428 (mmt) cc_final: 0.7215 (mpm) REVERT: G 86 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: G 180 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8049 (tt0) REVERT: G 229 MET cc_start: 0.8753 (ttm) cc_final: 0.8488 (ttp) REVERT: G 274 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7502 (mt) REVERT: G 371 LYS cc_start: 0.8158 (ttpt) cc_final: 0.7728 (ttpp) REVERT: G 393 ASP cc_start: 0.8227 (m-30) cc_final: 0.7837 (m-30) REVERT: G 431 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5023 (pt) REVERT: G 435 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.6632 (mtm180) REVERT: H 460 LYS cc_start: 0.8525 (ttpp) cc_final: 0.7841 (mppt) REVERT: H 470 LYS cc_start: 0.8576 (mtmt) cc_final: 0.8298 (mtpt) outliers start: 80 outliers final: 44 residues processed: 290 average time/residue: 0.6245 time to fit residues: 204.0203 Evaluate side-chains 271 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 216 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 273 GLU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 364 TYR Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 478 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 364 TYR Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 147 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 478 SER Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 184 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 218 optimal weight: 0.9990 chunk 210 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 48 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 149 optimal weight: 3.9990 chunk 201 optimal weight: 0.0970 chunk 192 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.164600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123383 restraints weight = 20205.098| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 1.92 r_work: 0.3234 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18746 Z= 0.128 Angle : 0.620 12.402 25454 Z= 0.283 Chirality : 0.046 0.187 2844 Planarity : 0.004 0.056 3200 Dihedral : 12.157 150.453 2800 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 3.01 % Allowed : 22.25 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.90 (0.17), residues: 2280 helix: -0.46 (0.19), residues: 788 sheet: -1.82 (0.22), residues: 446 loop : -1.54 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 451 TYR 0.014 0.001 TYR C 295 PHE 0.011 0.001 PHE C 112 TRP 0.009 0.001 TRP A 103 HIS 0.005 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00297 (18730) covalent geometry : angle 0.56161 (25406) hydrogen bonds : bond 0.03091 ( 574) hydrogen bonds : angle 5.19510 ( 1689) metal coordination : bond 0.00776 ( 16) metal coordination : angle 6.08605 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 237 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8796 (m-10) cc_final: 0.8504 (m-10) REVERT: A 149 VAL cc_start: 0.8491 (t) cc_final: 0.8248 (m) REVERT: A 154 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6966 (mt) REVERT: A 186 ASP cc_start: 0.7919 (m-30) cc_final: 0.7591 (m-30) REVERT: A 248 LYS cc_start: 0.7251 (mmmm) cc_final: 0.6948 (tppp) REVERT: B 373 MET cc_start: 0.7498 (mmt) cc_final: 0.7271 (mpm) REVERT: C 180 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7990 (tt0) REVERT: C 229 MET cc_start: 0.8668 (ttm) cc_final: 0.8379 (ttp) REVERT: C 295 TYR cc_start: 0.8487 (m-10) cc_final: 0.8280 (m-10) REVERT: C 371 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7774 (ttpp) REVERT: C 393 ASP cc_start: 0.8297 (m-30) cc_final: 0.7902 (m-30) REVERT: C 431 LEU cc_start: 0.5755 (OUTLIER) cc_final: 0.5135 (pt) REVERT: C 435 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.6761 (mtm180) REVERT: D 460 LYS cc_start: 0.8435 (ttpp) cc_final: 0.7903 (mppt) REVERT: D 470 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8333 (mtpt) REVERT: E 142 TYR cc_start: 0.8793 (m-10) cc_final: 0.8503 (m-10) REVERT: E 149 VAL cc_start: 0.8504 (t) cc_final: 0.8259 (m) REVERT: E 154 ILE cc_start: 0.7298 (OUTLIER) cc_final: 0.6960 (mt) REVERT: E 186 ASP cc_start: 0.7923 (m-30) cc_final: 0.7595 (m-30) REVERT: E 248 LYS cc_start: 0.7247 (mmmm) cc_final: 0.6946 (tppp) REVERT: F 373 MET cc_start: 0.7483 (mmt) cc_final: 0.7238 (mpm) REVERT: G 86 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7830 (pm20) REVERT: G 180 GLU cc_start: 0.8260 (mt-10) cc_final: 0.8011 (tt0) REVERT: G 229 MET cc_start: 0.8688 (ttm) cc_final: 0.8457 (ttp) REVERT: G 390 LEU cc_start: 0.8112 (tt) cc_final: 0.7898 (tp) REVERT: G 393 ASP cc_start: 0.8270 (m-30) cc_final: 0.7891 (m-30) REVERT: G 431 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5121 (pt) REVERT: G 435 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.6762 (mtm180) REVERT: H 460 LYS cc_start: 0.8447 (ttpp) cc_final: 0.7913 (mppt) REVERT: H 470 LYS cc_start: 0.8579 (mtmt) cc_final: 0.8304 (mtpt) outliers start: 58 outliers final: 30 residues processed: 285 average time/residue: 0.5863 time to fit residues: 188.5677 Evaluate side-chains 261 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 224 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 217 LEU Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 116 optimal weight: 0.5980 chunk 171 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 221 optimal weight: 0.0020 chunk 5 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 176 optimal weight: 0.0060 chunk 210 optimal weight: 3.9990 overall best weight: 0.8606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN C 211 ASN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN G 101 ASN G 118 GLN G 211 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.162485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121733 restraints weight = 20216.101| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.82 r_work: 0.3128 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18746 Z= 0.171 Angle : 0.639 12.059 25454 Z= 0.297 Chirality : 0.047 0.183 2844 Planarity : 0.004 0.059 3200 Dihedral : 12.244 149.851 2800 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.01 % Allowed : 22.82 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2280 helix: -0.42 (0.19), residues: 788 sheet: -1.77 (0.22), residues: 446 loop : -1.49 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 451 TYR 0.013 0.001 TYR G 295 PHE 0.012 0.001 PHE C 112 TRP 0.007 0.001 TRP E 103 HIS 0.006 0.001 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00403 (18730) covalent geometry : angle 0.58663 (25406) hydrogen bonds : bond 0.03292 ( 574) hydrogen bonds : angle 5.24372 ( 1689) metal coordination : bond 0.01356 ( 16) metal coordination : angle 5.89033 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8797 (m-10) cc_final: 0.8527 (m-10) REVERT: A 154 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6890 (mt) REVERT: A 158 LYS cc_start: 0.8351 (mtpm) cc_final: 0.7808 (pttt) REVERT: A 186 ASP cc_start: 0.7899 (m-30) cc_final: 0.7545 (m-30) REVERT: A 248 LYS cc_start: 0.7281 (mmmm) cc_final: 0.6994 (tppp) REVERT: B 373 MET cc_start: 0.7465 (mmt) cc_final: 0.7191 (mpm) REVERT: C 180 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8002 (tt0) REVERT: C 229 MET cc_start: 0.8760 (ttm) cc_final: 0.8478 (ttp) REVERT: C 295 TYR cc_start: 0.8531 (m-10) cc_final: 0.8265 (m-10) REVERT: C 371 LYS cc_start: 0.8177 (ttpt) cc_final: 0.7586 (ttpp) REVERT: C 393 ASP cc_start: 0.8262 (m-30) cc_final: 0.7826 (m-30) REVERT: C 431 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5151 (pt) REVERT: C 435 ARG cc_start: 0.7614 (OUTLIER) cc_final: 0.6628 (mtm180) REVERT: D 460 LYS cc_start: 0.8468 (ttpp) cc_final: 0.7846 (mppt) REVERT: E 142 TYR cc_start: 0.8795 (m-10) cc_final: 0.8531 (m-10) REVERT: E 154 ILE cc_start: 0.7251 (OUTLIER) cc_final: 0.6884 (mt) REVERT: E 158 LYS cc_start: 0.8348 (mtpm) cc_final: 0.7799 (pttt) REVERT: E 186 ASP cc_start: 0.7906 (m-30) cc_final: 0.7550 (m-30) REVERT: E 248 LYS cc_start: 0.7271 (mmmm) cc_final: 0.6987 (tppp) REVERT: F 373 MET cc_start: 0.7465 (mmt) cc_final: 0.7153 (mpm) REVERT: G 86 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7849 (pm20) REVERT: G 180 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8024 (tt0) REVERT: G 229 MET cc_start: 0.8783 (ttm) cc_final: 0.8507 (ttp) REVERT: G 390 LEU cc_start: 0.8043 (tt) cc_final: 0.7829 (tp) REVERT: G 393 ASP cc_start: 0.8235 (m-30) cc_final: 0.7846 (m-30) REVERT: G 431 LEU cc_start: 0.5788 (OUTLIER) cc_final: 0.5135 (pt) REVERT: G 435 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.6623 (mtm180) REVERT: H 460 LYS cc_start: 0.8476 (ttpp) cc_final: 0.7847 (mppt) REVERT: H 470 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8234 (mtpt) outliers start: 58 outliers final: 31 residues processed: 266 average time/residue: 0.6155 time to fit residues: 185.0926 Evaluate side-chains 250 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 374 MET Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Chi-restraints excluded: chain H residue 525 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 212 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 224 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 202 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 24 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN ** D 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.162972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121560 restraints weight = 20268.243| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.91 r_work: 0.3077 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18746 Z= 0.163 Angle : 0.639 12.590 25454 Z= 0.295 Chirality : 0.047 0.183 2844 Planarity : 0.004 0.059 3200 Dihedral : 12.254 150.524 2800 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.34 % Allowed : 23.34 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.79 (0.17), residues: 2280 helix: -0.37 (0.19), residues: 788 sheet: -1.76 (0.22), residues: 446 loop : -1.46 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 451 TYR 0.016 0.001 TYR E 99 PHE 0.011 0.001 PHE C 112 TRP 0.007 0.001 TRP A 103 HIS 0.006 0.001 HIS F 304 Details of bonding type rmsd covalent geometry : bond 0.00383 (18730) covalent geometry : angle 0.58344 (25406) hydrogen bonds : bond 0.03264 ( 574) hydrogen bonds : angle 5.22986 ( 1689) metal coordination : bond 0.01244 ( 16) metal coordination : angle 6.01897 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 TYR cc_start: 0.8814 (m-10) cc_final: 0.8550 (m-10) REVERT: A 154 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6935 (mt) REVERT: A 158 LYS cc_start: 0.8337 (mtpm) cc_final: 0.7816 (pttt) REVERT: A 186 ASP cc_start: 0.7933 (m-30) cc_final: 0.7587 (m-30) REVERT: A 248 LYS cc_start: 0.7253 (mmmm) cc_final: 0.7025 (tppp) REVERT: B 370 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7184 (tt) REVERT: B 373 MET cc_start: 0.7544 (mmt) cc_final: 0.7222 (mpm) REVERT: C 180 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8031 (tt0) REVERT: C 229 MET cc_start: 0.8792 (ttm) cc_final: 0.8533 (ttp) REVERT: C 295 TYR cc_start: 0.8439 (m-10) cc_final: 0.8214 (m-10) REVERT: C 371 LYS cc_start: 0.8187 (ttpt) cc_final: 0.7640 (ttpp) REVERT: C 393 ASP cc_start: 0.8321 (m-30) cc_final: 0.7970 (m-30) REVERT: C 431 LEU cc_start: 0.5816 (OUTLIER) cc_final: 0.5161 (pt) REVERT: C 435 ARG cc_start: 0.7615 (OUTLIER) cc_final: 0.6633 (mtm180) REVERT: D 460 LYS cc_start: 0.8495 (ttpp) cc_final: 0.7866 (mppt) REVERT: E 142 TYR cc_start: 0.8813 (m-10) cc_final: 0.8554 (m-10) REVERT: E 154 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6928 (mt) REVERT: E 158 LYS cc_start: 0.8332 (mtpm) cc_final: 0.7806 (pttt) REVERT: E 186 ASP cc_start: 0.7941 (m-30) cc_final: 0.7587 (m-30) REVERT: E 248 LYS cc_start: 0.7254 (mmmm) cc_final: 0.7025 (tppp) REVERT: F 370 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7178 (tt) REVERT: F 373 MET cc_start: 0.7467 (mmt) cc_final: 0.7153 (mpm) REVERT: G 86 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7877 (pm20) REVERT: G 180 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8038 (tt0) REVERT: G 229 MET cc_start: 0.8809 (ttm) cc_final: 0.8556 (ttp) REVERT: G 390 LEU cc_start: 0.8095 (tt) cc_final: 0.7878 (tp) REVERT: G 393 ASP cc_start: 0.8294 (m-30) cc_final: 0.7924 (m-30) REVERT: G 431 LEU cc_start: 0.5807 (OUTLIER) cc_final: 0.5153 (pt) REVERT: G 435 ARG cc_start: 0.7609 (OUTLIER) cc_final: 0.6628 (mtm180) REVERT: H 460 LYS cc_start: 0.8498 (ttpp) cc_final: 0.7868 (mppt) REVERT: H 470 LYS cc_start: 0.8519 (mtmt) cc_final: 0.8230 (mtpt) outliers start: 45 outliers final: 32 residues processed: 255 average time/residue: 0.6374 time to fit residues: 182.4625 Evaluate side-chains 253 residues out of total 1924 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 212 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 501 VAL Chi-restraints excluded: chain B residue 539 ILE Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 135 ASP Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 382 GLN Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 435 ARG Chi-restraints excluded: chain D residue 472 SER Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 291 ILE Chi-restraints excluded: chain F residue 370 LEU Chi-restraints excluded: chain F residue 501 VAL Chi-restraints excluded: chain F residue 539 ILE Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 86 GLU Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 239 VAL Chi-restraints excluded: chain G residue 374 MET Chi-restraints excluded: chain G residue 382 GLN Chi-restraints excluded: chain G residue 409 VAL Chi-restraints excluded: chain G residue 431 LEU Chi-restraints excluded: chain G residue 435 ARG Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 508 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 148 optimal weight: 2.9990 chunk 203 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 181 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 124 optimal weight: 0.0370 chunk 184 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 ASN B 359 ASN C 101 ASN C 118 GLN F 355 ASN F 359 ASN G 101 ASN G 118 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.164166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122894 restraints weight = 20303.838| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.91 r_work: 0.3126 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18746 Z= 0.141 Angle : 0.628 12.169 25454 Z= 0.289 Chirality : 0.046 0.184 2844 Planarity : 0.004 0.057 3200 Dihedral : 12.172 152.116 2800 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.65 % Allowed : 23.28 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.17), residues: 2280 helix: -0.22 (0.19), residues: 774 sheet: -1.74 (0.22), residues: 448 loop : -1.43 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 451 TYR 0.016 0.001 TYR G 295 PHE 0.011 0.001 PHE C 112 TRP 0.008 0.001 TRP E 103 HIS 0.007 0.001 HIS F 304 Details of bonding type rmsd covalent geometry : bond 0.00330 (18730) covalent geometry : angle 0.57057 (25406) hydrogen bonds : bond 0.03187 ( 574) hydrogen bonds : angle 5.17140 ( 1689) metal coordination : bond 0.00951 ( 16) metal coordination : angle 6.04571 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7164.03 seconds wall clock time: 122 minutes 50.01 seconds (7370.01 seconds total)